Atm, I still think the dystopian future will be an alternate timeline, and for that future what we saw in X1 to X3 either did not happen or did not happen in quite the same way, as the event that is being changed to actively prevent that future occurs in 1973, before the original trilogy.

So, for the original trilogy to stand intact, that change has already taken place in it's past.

This would allow for them to have Xavier alive in the future without having to refute X3, or expand on the post credits mind swap nonsense (which would also require explanation of Moira's presence there). Rogue can still be powered, etc.

What this would mean for the film is that in changing the past of 1973 they basically set up the world of X1 to X3...which doesn't end all that well...

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